Research Articles

Submitted on November 1, 2004
Accepted on December 14, 2004

The Selective Cause of an Ancient Adaptation

Guoping Zhu ¹, G. Brian Golding ², Antony M. Dean ^3*

¹ BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
² Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
³ BioTechnology Institute & the Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.

^* To whom correspondence should be addressed.
Antony M. Dean , E-mail: adean{at}biosci.umn.edu

Present address: Department of Biology, Anhui Normal University, Wuhu 241000, Peoples Republic of China.

Phylogenetic analysis reveals that NADP use by prokaryotic isocitrate dehydrogenase arose around the time eukaryotic mitochondria first appeared, some 3.5 billion years ago. We replaced the wildtype gene encoding the NADP-dependent isocitrate dehydrogenase of Escherichia coli by an engineered one possessing the ancestral NAD-dependent phenotype. The engineered enzyme is disfavored during competition for acetate. The selection intensifies in genetic backgrounds where other sources of reduced NADP have been removed. A survey of sequenced prokaryotic genomes reveals that those encoding isocitrate lyase, which is essential for growth on acetate, always have an NADP-dependent isocitrate dehydrogenase. Those with only an NAD-dependent isocitrate dehydrogenase never have isocitrate lyase. Hence, the NADP-dependence of prokaryotic isocitrate dehydrogenase is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate.

Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility.

P. E. Tomatis, S. M. Fabiane, F. Simona, P. Carloni, B. J. Sutton, and A. J. Vila (2008)
PNAS 105, 20605-20610
 |  Abstract »  |  Full Text »  |  PDF »

Evolution of Hormone Signaling in Elasmobranchs by Exploitation of Promiscuous Receptors.

S. M. Carroll, J. T. Bridgham, and J. W. Thornton (2008)
Mol. Biol. Evol. 25, 2643-2652
 |  Abstract »  |  Full Text »  |  PDF »

From the Cover: Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates.

S. Yokoyama, T. Tada, H. Zhang, and L. Britt (2008)
PNAS 105, 13480-13485
 |  Abstract »  |  Full Text »  |  PDF »

Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters.

A. Wagner (2007)
Genetics 176, 2451-2463
 |  Abstract »  |  Full Text »  |  PDF »

Direct demonstration of an adaptive constraint..

S. P. Miller, M. Lunzer, and A. M. Dean (2006)
Science 314, 458-461
 |  Abstract »  |  Full Text »  |  PDF »

Evolution of hormone-receptor complexity by molecular exploitation..

J. T. Bridgham, S. M. Carroll, and J. W. Thornton (2006)
Science 312, 97-101
 |  Abstract »  |  Full Text »  |  PDF »

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling.

R. Mahadevan, D. R. Bond, J. E. Butler, A. Esteve-Nunez, M. V. Coppi, B. O. Palsson, C. H. Schilling, and D. R. Lovley (2006)
Appl. Envir. Microbiol. 72, 1558-1568
 |  Abstract »  |  Full Text »  |  PDF »

The Biochemical Architecture of an Ancient Adaptive Landscape.

M. Lunzer, S. P. Miller, R. Felsheim, and A. M. Dean (2005)
Science 310, 499-501
 |  Abstract »  |  Full Text »  |  PDF »

Crystal Structure of Tetrameric Homoisocitrate Dehydrogenase from an Extreme Thermophile, Thermus thermophilus: Involvement of Hydrophobic Dimer-Dimer Interaction in Extremely High Thermotolerance.

J. Miyazaki, K. Asada, S. Fushinobu, T. Kuzuyama, and M. Nishiyama (2005)
J. Bacteriol. 187, 6779-6788
 |  Abstract »  |  Full Text »  |  PDF »

Location of the Coenzyme Binding Site in the Porcine Mitochondrial NADP-dependent Isocitrate Dehydrogenase.

Y. C. Huang and R. F. Colman (2005)
J. Biol. Chem. 280, 30349-30353
 |  Abstract »  |  Full Text »  |  PDF »

To Advertise   |   Find Products